Enzymes Flashcards
What is an enzyme and what does it do
- a biological catalyst which speeds up rate of reactions by providing alternate pathways with lower Ea and remain unchanged itself at the end of the reaction
6 classes of enzymes and what they do
1 oxidoreductases -catalyze redox reactions
2 lyases - catalyze cleavage of C-C, C-N and C-S bonds. Break double bonds and add groups. Form double bonds by removing groups
3 hydrolyases- cleave bonds and add H2O
4 ligase- ATP dependent to form bonds between C and O, S and N
5 transferase -transfers P, C or N containing groups
6 isomerase - rearranges atoms in a molecules to produce isomers
Diff between synthetase and synthase
- requires ATP
- atp independent
Diff between phosphatase and phosphorylase
- uses H20 to hydrolyze / remove phosphoryl group
- used Pi to cleave bonds and produce phosphorylated product
Diff between oxidase and oxygenase
- O2 is acceptor and oxygen atoms not added to substrate
- one or both oxygen atoms added to substrate
What does dehydrogenase do
-NAD+ / FAD is the electron receptor in redox reaction
Define active site , how formed and function
- clefts in enzymes formed by folding of protein
- has aas side groups to bind to substrate and participate in catalysis
What is Kcat
-number of substrate converted to product per enzyme molecule per second
Describe catalytic efficient and specificity of enzymes
- enzyme catalyzed reactions are very efficient
- they interact with specific substrates and catalyze specific reactions
What is holoenzyme , apo enzyme , cofactor and coenzyme
- active enzyme and its non-protein components
- inactive protein part of enzyme without its non-protein component
- non protein moiety of enzyme which is a metal ion
- non protein moiety of enzyme which is a small molecule
Define cosubstrate and prothestic group
- co enzyme which associates with enzyme for a short time and dissociates from enzyme in a altered state
- co enzyme permanently associated with enzyme and returns to original form
How does location of enzymes within cell aid in its functions
- isolates substrate from product from other competing reactions
- favorable environment for reactions
What do enzymes accelerate and what don’t they change
- rate at which equilibrium is reached
- do not alter equilibrium of reaction
What do active sites do and how do they aid in catalysis
/they bind to substrate through aas R groups
1 binds to substrate and rearranges bonds reducing Ea
2 stabilize transition state and increase conc of intermediate than can be formed into products
3 enclose substrate and separate it from solution , competing reaction sand provide favorable conditions
List Factors affecting reaction velocity
1 pH
2 temperature
3 substrate concentration
Shape taken by allosteric enzyme and non on Vo against substrate graph
- sigmoid
- hyperbolic
What is denaturation and how does pH denature
- structural change in protein resulting in loss of biological properties
- active sites depend on ionic nature of side groups
What does the Michaelis-Menten equation describe
-how reaction velocity varies with substrate concentration
Assumption in deriving M-M equation
1 conc of E lower than S so few % of S are bound to enzyme
2 ES conc doesn’t change : steady state assumption
3 initial velocity measured as soon as E and S mix. Conc P small so backward rate of reaction is ignored
What is Km
-characteristic of enzymes and substrate showing the affinity and enzyme has for a substrate
Conclusions of small and large Km
- high affinity for substrate as low S conc is needed to half saturate E
- low affinity as high S conc needed to half saturate enzyme
What is Km equal to numerically
-conc off S at which velocity is 1/2 vmax
What is Vmax
-maximal rate of reaction at which all binding sites are bound to substrates and are constantly being reoccupied
Relation of velocity to enzyme conc
-directly proportional
Order of reaction when conc S is less than , equal to and greater than Km
- velocity is directly proportional to conc S ( 1st order )
- velocity constant and equal to Vmax ( 0 order and velocity independent to conc S )
Line weaver-Burk plot function and why !?
- straight line used to find Km, Vmax and determine mechanism of action of enzyme inhibitors
- not possible to determine Vmax on Vo against S graph due to gradual upward slope or hyperbolic graph
What are enzyme inhibitors
-any substance that decrease velocity of enzyme catalyze reactions
Types of inhibitors and how they bind to enzyme
1 irreversible- covalent bonds with enzyme
2 reversible - non covalent bonds
Describe suicide inhibitors
-mechanism based inhibitors that are converted by enzyme to a form that covalently links to enzymes
Two types of inhibitors and the extra one
1 competitive
2 non competitive
3 mixed
Competitive inhibitors mode of action and effect on Vmax, Km and Lineweaver-Burk plot
-binds reversibly to same site as substrate. Competes with substrate for active site
- effect on Vmax reversed by increase in S conc
- Apparent Km is increased as more S conc needed to reach half Vmax
- Vmax unchanged but Km different
Competitive inhibitors mode of action and effect on Vmax, Km and Lineweaver-Burk plot
- inhibitors bind to site diff to active site of substrate
- can bind free enzyme or ES complex
- Vmax reduced and cannot be reversed by increase in S conc
- do not interfere with binding of substrate so Km is same
- Km unchanged but Vmax diff
What are transition analogs
-competitive inhibitors which approximate structure of transition state and bind to enzyme with higher affinity than substrate
Describe statin drugs, types and what they do
- anti hyper lipidemic drugs
- competitive inhibitors for HMG-CoA ( enzyme for cholesterol biosynthesis )
- atorvastatin and pravastatin
- inhibit cholesterol synthesis
What is an allosteric enzyme
Allosteric enzymes are enzymes that change their conformational ensemble upon binding of an effector which results in an apparent change in binding affinity at a different ligand binding site
What are effectors
-molecules which bind to site other than active site
Classes of effectors and their outcomes
What do they affect
- positive : increase enzyme activity
- negative: decrease enzyme activity
- affect affinity for substrate or maximal rate of catalysis
Types of effectors and describe them
1 homotropic - effectors is substrate. It binds at one site and affects properties of another site
( cooperativity )
2 heterotrophic - effector diff from enzyme
Regulation by covalent modification example and outcome
-activate or inhibit enzyme activity
Describe induction and repression and of enzymes and outcome
Cells can either induct ( synthesize) or repress ( degrade ) enzymes affecting number of active sites available
What is a transition state
- a transient molecule where either decay to S or P is equally possible
- no stable and no finite chemical lifespan
What is a reaction intermediate
What is reaction step
What determines overall rate of reaction
- has finite chemical lifespan , can be isolated
- interconversion between 2 subsequent intermediates or transitions states
- step/ steps with the highest Ea. Rate determining / limiting step
How do enzymes reduce Ea
- covalent bonds between enzyme active site aas side groups and substrate rearranges bonds weakening them and lowering Ea
- numerous non covalent forces between enzymes and substrate ( no reacting parts included ) is accompanied by release of binding energy which compensates for Ea and lowers it
Where are weak non covalent bonds optimized and why
At transition state of substrate
-the numerous bonds release binding energy used to compensate formation of transition state and lower Ea. ES partially stabilized so not much Ea added to overcome
What won’t enzyme complimentary to substrate won’t work
-numerous non covalent forces overly stabilize the ES complex and when forming the transition state numerous bonds have to be now broken on ES complex and Ea is increase instead
Explain what is and how specificity of enzymes arises
- ability of enzymes to differentiate between substrates and reactions
- the numerous non covalent forces as positioned on an enzyme form maximal when paired with a specific substrate and not with another thus bringing about specificity
List the barriers to be overcome in a enzyme catalyze reaction
1 reduction in entropy - decrease free movement of reacting molecules
2 solvation shell of water that surrounds and stabilized some biomolecules
3 distortion of substrate
4 conformational changes on enzymes to properly align with substrate
What overcomes barriers to enzyme catalyze reactions and how
Binding energy
1 Substrates clamped in place by weak non covalent interactions with it and enzyme functional groups
2 formation of E and S weak bonds replaces water bonds thus desolving substrate
3 binding energy compensates any energy needed to distort S
4 Enzymes undergo multiple conformations to align functional groups properly when bound to Substrate by weak covalent forces - induced fit
How does specific catalytic groups differ from binding energy and list the 3 types of specific catalytic groups
-they form transient covalent bonds or transfer of groups
To and fro substrate
1 metal ion
2 covalent catalysis
3 acid-base catalysis
Describe covalent catalysis
- transient covalent bond formed between E and S.
- E has nucleophilic group X
- always undergo further reaction needed to liberate enzyme
Describe metal ion catalysis
- enzyme bound metal ion and substrate interactions can orient S for reaction or stabilize transition state
- can mediate redox reactions by reversible changes in metal oxidation states
How can charges intermediates be stabilized
-transfer of protons to and fro intermediate to form species that is stable and can easily break down into product
Describe specific acid-base catalysis
- protein donor and acceptor is water ( H+ and OH- )
- if protons transferred to and fro intermediate faster than it can break down into reactants then it us stabilized
Describe general acid-base catalysis
-proton transfer mediated by other molecules when water doesn’t suffice
What acts as proton donor and acceptor in enzymes
-aas side chains
